//
// Manta - Structural Variant and Indel Caller
// Copyright (c) 2013-2019 Illumina, Inc.
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program.  If not, see <http://www.gnu.org/licenses/>.
//
//

/// \file
/// \author Chris Saunders
///

#pragma once

#include "common/Program.hpp"

#include <string>

struct DSLOptions {
  DSLOptions() : isLocusIndex(false), locusIndex(0) {}

  bool        isLocusIndex = false;
  unsigned    locusIndex   = 0;
  std::string graphFilename;
  std::string locusFilename;
  std::string region;
};

void parseDSLOptions(const illumina::Program& prog, int argc, char* argv[], DSLOptions& opt);
